Examples with ImageTypeSetting qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting used on opensource projects

Example 1 with ImageTypeSetting

use of qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting in project qupath by qupath.

the class ImageDetailsPane method promptToSetImageType.

// /**
// * Prompt the user to set the {@link ImageType} for the image.
// * @param imageData
// * @return
// */
// public static boolean promptToSetImageType(ImageData<BufferedImage> imageData) {
// List<ImageType> values = Arrays.asList(ImageType.values());
// if (!imageData.getServer().isRGB()) {
// values = new ArrayList<>(values);
// values.remove(ImageType.BRIGHTFIELD_H_DAB);
// values.remove(ImageType.BRIGHTFIELD_H_E);
// values.remove(ImageType.BRIGHTFIELD_OTHER);
// }
// 
// var dialog = new ChoiceDialog<>(imageData.getImageType(), values);
// dialog.setTitle("Image type");
// if (QuPathGUI.getInstance() != null)
// dialog.initOwner(QuPathGUI.getInstance().getStage());
// dialog.getDialogPane().setHeaderText(null);
// dialog.getDialogPane().setContentText("Set image type");
// dialog.getDialogPane().setPrefWidth(400);
// 
// var labelExplain = new Label("The image type influences some commands (e.g. cell detection) and should be set for every image. "
// + "\n\nSelect an option below or in the preferences to customize how QuPath handles setting the image type when opening an image."
// + "\n\n'Auto-estimate' is convenient to reduce annoying prompts, but the estimates are sometimes wrong. "
// + "When this happens you can correct them by double-clicking "
// + "the type under the 'Image' tab.");
// labelExplain.setWrapText(true);
// labelExplain.setPrefWidth(400);
// labelExplain.setMinHeight(Label.USE_PREF_SIZE);
// 
// var comboSetType = new ComboBox<ImageTypeSetting>();
// comboSetType.getItems().setAll(ImageTypeSetting.values());
// comboSetType.getSelectionModel().select(PathPrefs.imageTypeSettingProperty().get());
// comboSetType.setMaxWidth(Double.MAX_VALUE);
// labelExplain.setPadding(new Insets(0, 0, 10, 0));
// var expandablePane = new BorderPane(labelExplain);
// expandablePane.setBottom(comboSetType);
// 
// dialog.getDialogPane().setExpandableContent(expandablePane);
// 
// var result = dialog.showAndWait();
// ImageType type = result.orElse(null);
// if (type == null)
// return false;
// 
// if (comboSetType.getSelectionModel().getSelectedItem() != null)
// PathPrefs.imageTypeSettingProperty().set(comboSetType.getSelectionModel().getSelectedItem());
// 
// if (type != imageData.getImageType()) {
// imageData.setImageType(type);
// return true;
// }
// return false;
// }
/**
 * Prompt the user to set the {@link ImageType} for the image.
 * @param imageData the image data for which the type should be set
 * @param defaultType the default type (selected when the dialog is shown)
 * @return true if the type was changed, false otherwise
 */
public static boolean promptToSetImageType(ImageData<BufferedImage> imageData, ImageType defaultType) {
    double size = 32;
    var group = new ToggleGroup();
    boolean isRGB = imageData.getServer().isRGB();
    if (defaultType == null)
        defaultType = ImageType.UNSET;
    var buttonMap = new LinkedHashMap<ImageType, ToggleButton>();
    // TODO: Create a nicer icon for unspecified type
    var iconUnspecified = (Group) createImageTypeCell(Color.GRAY, null, null, size);
    if (isRGB) {
        buttonMap.put(ImageType.BRIGHTFIELD_H_E, createImageTypeButton(ImageType.BRIGHTFIELD_H_E, "Brightfield\nH&E", createImageTypeCell(Color.WHITE, Color.PINK, Color.DARKBLUE, size), "Brightfield image with hematoylin & eosin stains\n(8-bit RGB only)", isRGB));
        buttonMap.put(ImageType.BRIGHTFIELD_H_DAB, createImageTypeButton(ImageType.BRIGHTFIELD_H_DAB, "Brightfield\nH-DAB", createImageTypeCell(Color.WHITE, Color.rgb(200, 200, 220), Color.rgb(120, 50, 20), size), "Brightfield image with hematoylin & DAB stains\n(8-bit RGB only)", isRGB));
        buttonMap.put(ImageType.BRIGHTFIELD_OTHER, createImageTypeButton(ImageType.BRIGHTFIELD_OTHER, "Brightfield\nOther", createImageTypeCell(Color.WHITE, Color.ORANGE, Color.FIREBRICK, size), "Brightfield image with other chromogenic stains\n(8-bit RGB only)", isRGB));
    }
    buttonMap.put(ImageType.FLUORESCENCE, createImageTypeButton(ImageType.FLUORESCENCE, "Fluorescence", createImageTypeCell(Color.BLACK, Color.LIGHTGREEN, Color.BLUE, size), "Fluorescence or fluorescence-like image with a dark background\n" + "Also suitable for imaging mass cytometry", true));
    buttonMap.put(ImageType.OTHER, createImageTypeButton(ImageType.OTHER, "Other", createImageTypeCell(Color.BLACK, Color.WHITE, Color.GRAY, size), "Any other image type", true));
    buttonMap.put(ImageType.UNSET, createImageTypeButton(ImageType.UNSET, "Unspecified", iconUnspecified, "Do not set the image type (not recommended for analysis)", true));
    var buttons = buttonMap.values().toArray(ToggleButton[]::new);
    for (var btn : buttons) {
        if (btn.isDisabled()) {
            btn.getTooltip().setText("Image type is not supported because image is not RGB");
        }
    }
    var buttonList = Arrays.asList(buttons);
    group.getToggles().setAll(buttons);
    group.selectedToggleProperty().addListener((v, o, n) -> {
        // Ensure that we can't deselect all buttons
        if (n == null)
            o.setSelected(true);
    });
    PaneTools.setMaxWidth(Double.MAX_VALUE, buttons);
    PaneTools.setMaxHeight(Double.MAX_VALUE, buttons);
    var selectedButton = buttonMap.get(defaultType);
    group.selectToggle(selectedButton);
    var grid = new GridPane();
    int nHorizontal = 3;
    int nVertical = (int) Math.ceil(buttons.length / (double) nHorizontal);
    grid.getColumnConstraints().setAll(IntStream.range(0, nHorizontal).mapToObj(i -> {
        var c = new ColumnConstraints();
        c.setPercentWidth(100.0 / nHorizontal);
        return c;
    }).collect(Collectors.toList()));
    grid.getRowConstraints().setAll(IntStream.range(0, nVertical).mapToObj(i -> {
        var c = new RowConstraints();
        c.setPercentHeight(100.0 / nVertical);
        return c;
    }).collect(Collectors.toList()));
    grid.setVgap(5);
    // grid.setHgap(5);
    grid.setMaxWidth(Double.MAX_VALUE);
    for (int i = 0; i < buttons.length; i++) {
        grid.add(buttons[i], i % nHorizontal, i / nHorizontal);
    }
    // grid.getChildren().setAll(buttons);
    var content = new BorderPane(grid);
    var comboOptions = new ComboBox<ImageTypeSetting>();
    comboOptions.getItems().setAll(ImageTypeSetting.values());
    var prompts = Map.of(ImageTypeSetting.AUTO_ESTIMATE, "Always auto-estimate type (don't prompt)", ImageTypeSetting.PROMPT, "Always prompt me to set type", ImageTypeSetting.NONE, "Don't set the image type");
    comboOptions.setButtonCell(GuiTools.createCustomListCell(p -> prompts.get(p)));
    comboOptions.setCellFactory(c -> GuiTools.createCustomListCell(p -> prompts.get(p)));
    comboOptions.setTooltip(new Tooltip("Choose whether you want to see these prompts " + "when opening an image for the first time"));
    comboOptions.setMaxWidth(Double.MAX_VALUE);
    // comboOptions.prefWidthProperty().bind(grid.widthProperty().subtract(100));
    comboOptions.getSelectionModel().select(PathPrefs.imageTypeSettingProperty().get());
    if (nVertical > 1)
        BorderPane.setMargin(comboOptions, new Insets(5, 0, 0, 0));
    else
        BorderPane.setMargin(comboOptions, new Insets(10, 0, 0, 0));
    content.setBottom(comboOptions);
    var labelDetails = new Label("The image type is used for stain separation " + "by some commands, e.g. 'Cell detection'.\n" + "Brightfield types are only available for 8-bit RGB images.");
    // + "For 'Brightfield' images you can set the color stain vectors.");
    labelDetails.setWrapText(true);
    labelDetails.prefWidthProperty().bind(grid.widthProperty().subtract(10));
    labelDetails.setMaxHeight(Double.MAX_VALUE);
    labelDetails.setPrefHeight(Label.USE_COMPUTED_SIZE);
    labelDetails.setPrefHeight(100);
    labelDetails.setAlignment(Pos.CENTER);
    labelDetails.setTextAlignment(TextAlignment.CENTER);
    var dialog = Dialogs.builder().title("Set image type").headerText("What type of image is this?").content(content).buttons(ButtonType.APPLY, ButtonType.CANCEL).expandableContent(labelDetails).build();
    // Try to make it easier to dismiss the dialog in a variety of ways
    var btnApply = dialog.getDialogPane().lookupButton(ButtonType.APPLY);
    Platform.runLater(() -> selectedButton.requestFocus());
    for (var btn : buttons) {
        btn.setOnMouseClicked(e -> {
            if (!btn.isDisabled() && e.getClickCount() == 2) {
                btnApply.fireEvent(new ActionEvent());
                e.consume();
            }
        });
    }
    var enterPressed = new KeyCodeCombination(KeyCode.ENTER);
    var spacePressed = new KeyCodeCombination(KeyCode.SPACE);
    dialog.getDialogPane().addEventFilter(KeyEvent.KEY_PRESSED, e -> {
        if (enterPressed.match(e) || spacePressed.match(e)) {
            btnApply.fireEvent(new ActionEvent());
            e.consume();
        } else if (e.getCode() == KeyCode.UP || e.getCode() == KeyCode.DOWN || e.getCode() == KeyCode.LEFT || e.getCode() == KeyCode.RIGHT) {
            var selected = (ToggleButton) group.getSelectedToggle();
            var ind = buttonList.indexOf(selected);
            var newSelected = selected;
            if (e.getCode() == KeyCode.UP && ind >= nHorizontal) {
                newSelected = buttonList.get(ind - nHorizontal);
            }
            if (e.getCode() == KeyCode.LEFT && ind > 0) {
                newSelected = buttonList.get(ind - 1);
            }
            if (e.getCode() == KeyCode.RIGHT && ind < buttonList.size() - 1) {
                newSelected = buttonList.get(ind + 1);
            }
            if (e.getCode() == KeyCode.DOWN && ind < buttonList.size() - nHorizontal) {
                newSelected = buttonList.get(ind + nHorizontal);
            }
            newSelected.requestFocus();
            group.selectToggle(newSelected);
            e.consume();
        }
    });
    var response = dialog.showAndWait();
    if (response.orElse(ButtonType.CANCEL) == ButtonType.APPLY) {
        PathPrefs.imageTypeSettingProperty().set(comboOptions.getSelectionModel().getSelectedItem());
        var selectedType = (ImageType) group.getSelectedToggle().getUserData();
        if (selectedType != imageData.getImageType()) {
            imageData.setImageType(selectedType);
            return true;
        }
    }
    return false;
}